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I am one of the contributors to the megathread who mentioned these two cases, so I'll try to answer this follow-up. My answer may focus a bit on legal doctrine and justice-watching, but ultimately we are dealing with decisions made by the justices.

Basically, your speculation sits firmly within the mainstream understanding of the Supreme Court's shifts on civil rights doctrine during the 1940s. In this view, before and just after Pearl Harbor, the Supreme Court was inclined to defer to government infringements on civil liberties because of concerns about national unity and security, particularly as the Axis seemed poised for victory. But as the war continued and the United States was winning, these concerns faded. Instead, the Court extended civil liberties in order to distinguish America as the land of freedom from the fascist, totalitarian states against which it struggled. For a basic political science course or a mandatory constitutional law course in the first year of law school, this is probably good enough.

But let's tell a more detailed and nuanced story. We'll start with a little bit about the Jehovah's Witnesses themselves. The Jehovah's Witnesses were a pretty new religious movement that had begun to take shape in the 1870s and had assumed their current name and form in 1931. Jehovah's Witnesses figure prominently in the U.S. Supreme Court's mid-20th century civil rights jurisprudence. Harlan Fiske Stone, who figures prominently in this story, wrote to a colleague on the Supreme Court, "I think the Jehovah's Witnesses ought to have an endowment in view of the aid they give us in solving the legal problems of civil liberties." The beliefs and practices of the Jehovah's Witnesses repeatedly came into conflict with government policies.

The cases we'll highlight concerned the religious prohibition on professing allegiance to worldly governments, which Jehovah's Witnesses considered a form of idolatry. Jehovah's Witnesses were by no means the first group of people in America to have such scruples; however, unlike some of the older groups such as the Amish that secluded themselves, they were a new religious movement and lived in close contact with mainstream society. Thus, when Jehovah's Witness children attended public schools (there were very few Jehovah's Witness-run private schools), they were called upon to participate in patriotic customs such as saluting the flag, participating in pledges of allegiance, and singing patriotic songs. Refusal to do so might lead to school discipline or expulsion, and households with expelled children could expect to receive further visits that might result in the children being institutionalized. Nonetheless, among Witnesses grassroots movement of refusing to participate arose, which the denomination's leader "Judge" Rutherford ratified with a national radio address in 1935. More Witnesses refused, and meanwhile public opinion turned further against the movement, which was also in some disrepute because of its concentrated proselytization and the perceived shiftlessness of some of its adherents. With war looming, more and more students were required to participate in more and more patriotic displays, while the Witnesses' pleas for exemptions largely fell on deaf ears.

This gets us to Minersville School District v. Gobitis (1940). A school district in Pennsylvania had required a flag salute by students. The Gobitas children as devout Witnesses had refused and were expelled, so their father filed a federal lawsuit. (Yes, the name was actually "Gobitas," but it got misspelled somewhere along the way.) This looked like an uphill battle. In four previous cases, the challengers had lost in the lower courts, and the Court simply issued terse per curiam (i.e., unsigned and not deeply explained) opinions affirming the dispositions below. In Gobitis, however, the district court and court of appeals had sided with the challengers. From the district court's opinion: "The refusal of these two earnest Christian children to salute the flag cannot even remotely prejudice or imperil the safety, health, morals, property, or personal rights of their fellows." The court of appeals said the school-required show of loyalty was similar to what went on in Nazi Germany. Here I should point out that the flag salutes of this era often involved an extended right arm similar to the "Sieg Heil" salute of the Nazis.

The Supreme Court heard argument: Rutherford insisted on arguing on behalf of his flock and harangued the court with a sermon, but an American Civil Liberties Union lawyer was allowed to give a more conventional argument. (The ACLU had supported the Witnesses in their legal struggles.)

At conference after argument, Justice Felix Frankfurter--a Jew born in Austria known for his personal patriotism to the country where he'd been naturalized--persuaded all but one of his fellows (most of whom were predisposed against the Witnesses) that national unity was an important interest and that the government had the power to compel schoolchildren to stand up and salute the flag. On the strength of that performance, Chief Justice Charles Evans Hughes, already planning to vote against the Witnesses, assigned Frankfurter to write the opinion. Only Stone, whom we met previously, dissented, so the final tally was 8-1. (We know that Justice Frank Murphy, appointed earlier that year, had begun writing a dissent, but decided to join the majority.)

In his opinion for the majority, Frankfurter (also a founding member of the ACLU) explained that he personally would not have supported the school board's "vulgar intrusion of law in the domain of conscience," but said it was not up to the Court to set policy. As Frankfurter further explained in a note to Stone, "Constitutional power is on one side and my private notions of liberty and toleration and good sense are on the other." But ultimately, as Frankfurter wrote in his opinion, the government was doing something the constitution allowed, and the constitution did not require an exemption for the Witnesses. If they did not like it, the Witnesses could change their on views, stop going to public school, or try to prevail through the democratic process by explaining their concerns to their fellow citizens. According to one of Frankfurter's clerks, this was called in chambers "Felix's Fall of France Opinion" because it was written as Allied fortunes in Europe were at their lowest ebb.

But we can also say that his Gobitis opinion was consistent with Frankfurter's views of the judicial role and government power. During his career on the Supreme Court from 1939 to 1962, Frankfurter believed in judicial restraint, placing himself in a line of American jurisprudential thought perhaps most strongly associated with his friend and mentor Justice Oliver Wendell Holmes, Jr., also Louis D. Brandeis (the first Jewish justice and another friend and mentor). In this view, judges should resist the temptation to substitute their own judgment for that of democratic majorities.

In the context of Frankfurter's appointment, judicial restraint was regarded as progressive position favorable to the priorities of President Franklin Delano Roosevelt's New Deal and the Democrats who supported it. Bear in mind that the Supreme Court up to the mid-1930s had a significant record of striking down federal and state legislation, particularly economic regulation. We sometimes shorthand this a "Lochnerism" in reference to the notorious case Lochner v. New York (1905) in which the Supreme Court struck down a state law setting maximum hours bakers may work. (Holmes wrote a famous dissent chastising the Court for substituting its own judgment for a state legislature's.) Indeed, the Hughes court and its conservative wing known as the "Four Horsemen" had been so effective at blocking the New Deal agenda that Roosevelt had considered "packing" the Court with additional justices who would vote his way. Frankfurter, who had been a trusted advisor to Roosevelt during the struggles to implement the New Deal, could expected to reject Lochnerism and practice judicial restraint. On the other hand, some liberals (above all Frankfurter's friend Archibald MacLeish, then Librarian of Congress) also expected the new justice to stand up for civil rights, who--remember--had been a founder of the ACLU. They were to be disappointed.